Multiple sequence alignment - TraesCS5D01G174900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G174900 chr5D 100.000 3296 0 0 1 3296 274573580 274570285 0.000000e+00 6087
1 TraesCS5D01G174900 chr5D 82.866 998 142 21 1103 2084 275195251 275196235 0.000000e+00 869
2 TraesCS5D01G174900 chr5D 79.143 1237 217 29 1131 2343 275147027 275148246 0.000000e+00 817
3 TraesCS5D01G174900 chr5D 78.040 1143 202 31 1169 2287 275404801 275405918 0.000000e+00 675
4 TraesCS5D01G174900 chr5A 92.337 3367 150 45 6 3296 363599567 363596233 0.000000e+00 4689
5 TraesCS5D01G174900 chr5A 81.172 1195 199 18 1109 2287 364198632 364199816 0.000000e+00 937
6 TraesCS5D01G174900 chr5A 79.207 1236 218 28 1131 2343 363919804 363921023 0.000000e+00 822
7 TraesCS5D01G174900 chr5A 78.522 1150 194 42 1169 2287 364349567 364350694 0.000000e+00 706
8 TraesCS5D01G174900 chr5B 94.908 2612 65 31 735 3296 309666218 309663625 0.000000e+00 4024
9 TraesCS5D01G174900 chr5B 81.001 1179 196 21 1126 2287 312261198 312262365 0.000000e+00 911
10 TraesCS5D01G174900 chr5B 79.628 1237 211 29 1131 2343 309817031 309818250 0.000000e+00 850
11 TraesCS5D01G174900 chr5B 83.547 857 124 14 1437 2287 310035239 310036084 0.000000e+00 785
12 TraesCS5D01G174900 chr5B 78.659 1148 196 37 1169 2287 312592519 312593646 0.000000e+00 717
13 TraesCS5D01G174900 chr5B 89.486 428 41 4 162 588 309674207 309673783 3.740000e-149 538


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G174900 chr5D 274570285 274573580 3295 True 6087 6087 100.000 1 3296 1 chr5D.!!$R1 3295
1 TraesCS5D01G174900 chr5D 275195251 275196235 984 False 869 869 82.866 1103 2084 1 chr5D.!!$F2 981
2 TraesCS5D01G174900 chr5D 275147027 275148246 1219 False 817 817 79.143 1131 2343 1 chr5D.!!$F1 1212
3 TraesCS5D01G174900 chr5D 275404801 275405918 1117 False 675 675 78.040 1169 2287 1 chr5D.!!$F3 1118
4 TraesCS5D01G174900 chr5A 363596233 363599567 3334 True 4689 4689 92.337 6 3296 1 chr5A.!!$R1 3290
5 TraesCS5D01G174900 chr5A 364198632 364199816 1184 False 937 937 81.172 1109 2287 1 chr5A.!!$F2 1178
6 TraesCS5D01G174900 chr5A 363919804 363921023 1219 False 822 822 79.207 1131 2343 1 chr5A.!!$F1 1212
7 TraesCS5D01G174900 chr5A 364349567 364350694 1127 False 706 706 78.522 1169 2287 1 chr5A.!!$F3 1118
8 TraesCS5D01G174900 chr5B 309663625 309666218 2593 True 4024 4024 94.908 735 3296 1 chr5B.!!$R1 2561
9 TraesCS5D01G174900 chr5B 312261198 312262365 1167 False 911 911 81.001 1126 2287 1 chr5B.!!$F3 1161
10 TraesCS5D01G174900 chr5B 309817031 309818250 1219 False 850 850 79.628 1131 2343 1 chr5B.!!$F1 1212
11 TraesCS5D01G174900 chr5B 310035239 310036084 845 False 785 785 83.547 1437 2287 1 chr5B.!!$F2 850
12 TraesCS5D01G174900 chr5B 312592519 312593646 1127 False 717 717 78.659 1169 2287 1 chr5B.!!$F4 1118

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
277 292 0.033405 TTGGGGTGACACCGGAAAAA 60.033 50.0 18.4 5.41 39.83 1.94 F
382 397 0.104120 TGGGACGACATTAGGCATCG 59.896 55.0 0.0 0.00 41.60 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2309 0.463833 CCCCGTACTCTTTGCCATCC 60.464 60.000 0.00 0.00 0.00 3.51 R
2391 2481 9.202273 ACGCAAACACATATATGAAAATGTTTT 57.798 25.926 20.91 10.64 37.99 2.43 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 0.392863 TGGCTCATCGGTTCATGTGG 60.393 55.000 0.00 0.00 0.00 4.17
127 128 1.718757 GGCTCATCGGTTCATGTGGC 61.719 60.000 0.00 0.00 36.18 5.01
130 131 0.324614 TCATCGGTTCATGTGGCACT 59.675 50.000 19.83 1.19 0.00 4.40
133 134 0.396435 TCGGTTCATGTGGCACTCTT 59.604 50.000 19.83 0.59 0.00 2.85
148 149 6.983890 GTGGCACTCTTTTTGAAAAATAAGGA 59.016 34.615 11.13 0.00 0.00 3.36
151 152 6.646653 GCACTCTTTTTGAAAAATAAGGAGGG 59.353 38.462 16.58 14.66 0.00 4.30
152 153 7.471399 GCACTCTTTTTGAAAAATAAGGAGGGA 60.471 37.037 18.19 4.81 0.00 4.20
158 159 4.183916 TGAAAAATAAGGAGGGAGGAGGT 58.816 43.478 0.00 0.00 0.00 3.85
172 187 6.424032 AGGGAGGAGGTGAACATATTTTTAC 58.576 40.000 0.00 0.00 0.00 2.01
206 221 7.923878 GCTTATAAGGCTAATAGGATCTGCTAC 59.076 40.741 14.28 0.00 0.00 3.58
230 245 1.063942 GGTGTTTATGAAGGGAGGGGG 60.064 57.143 0.00 0.00 0.00 5.40
260 275 4.635324 ACAGGGAAAGCACAAACAAAATTG 59.365 37.500 0.00 0.00 36.37 2.32
265 280 2.916640 AGCACAAACAAAATTGGGGTG 58.083 42.857 0.00 4.39 42.45 4.61
273 288 0.186386 AAAATTGGGGTGACACCGGA 59.814 50.000 18.40 7.07 39.83 5.14
274 289 0.186386 AAATTGGGGTGACACCGGAA 59.814 50.000 18.40 13.15 39.83 4.30
277 292 0.033405 TTGGGGTGACACCGGAAAAA 60.033 50.000 18.40 5.41 39.83 1.94
284 299 3.506067 GGTGACACCGGAAAAATCTTGAT 59.494 43.478 9.46 0.00 0.00 2.57
293 308 4.498682 CGGAAAAATCTTGATCCATGCCTC 60.499 45.833 0.00 0.00 32.08 4.70
311 326 7.256475 CCATGCCTCTAGGATAGTTCTACAAAT 60.256 40.741 0.00 0.00 40.38 2.32
316 331 8.919145 CCTCTAGGATAGTTCTACAAATGAAGT 58.081 37.037 0.00 0.00 40.38 3.01
317 332 9.743057 CTCTAGGATAGTTCTACAAATGAAGTG 57.257 37.037 0.00 0.00 40.38 3.16
318 333 8.198109 TCTAGGATAGTTCTACAAATGAAGTGC 58.802 37.037 0.00 0.00 40.38 4.40
361 376 4.819105 AGGACATCCTCGACAATGTTTA 57.181 40.909 8.81 0.00 44.77 2.01
363 378 5.745227 AGGACATCCTCGACAATGTTTATT 58.255 37.500 8.81 0.00 44.77 1.40
368 383 4.258543 TCCTCGACAATGTTTATTGGGAC 58.741 43.478 5.17 0.00 46.33 4.46
374 389 5.391523 CGACAATGTTTATTGGGACGACATT 60.392 40.000 5.17 0.00 46.33 2.71
382 397 0.104120 TGGGACGACATTAGGCATCG 59.896 55.000 0.00 0.00 41.60 3.84
387 402 1.206132 ACGACATTAGGCATCGGTTGA 59.794 47.619 0.00 0.00 40.16 3.18
409 425 4.590487 TCGAAAGACCATGACGCC 57.410 55.556 0.00 0.00 33.31 5.68
410 426 1.668867 TCGAAAGACCATGACGCCA 59.331 52.632 0.00 0.00 33.31 5.69
421 437 4.373116 GACGCCACGGCTCTTCCA 62.373 66.667 6.48 0.00 39.32 3.53
422 438 3.876589 GACGCCACGGCTCTTCCAA 62.877 63.158 6.48 0.00 39.32 3.53
423 439 3.121030 CGCCACGGCTCTTCCAAG 61.121 66.667 6.48 0.00 39.32 3.61
437 453 1.151450 CCAAGCCCCCGAATAGCAT 59.849 57.895 0.00 0.00 0.00 3.79
438 454 0.890996 CCAAGCCCCCGAATAGCATC 60.891 60.000 0.00 0.00 0.00 3.91
452 468 1.115930 AGCATCGAGATAAGGGCGGT 61.116 55.000 0.00 0.00 0.00 5.68
453 469 0.946221 GCATCGAGATAAGGGCGGTG 60.946 60.000 0.00 0.00 39.03 4.94
469 485 3.385384 TGGAGAGCAGGCACGGAG 61.385 66.667 0.00 0.00 0.00 4.63
551 567 2.158900 AGAACCACACTCCAGACACTTG 60.159 50.000 0.00 0.00 0.00 3.16
607 623 8.143835 TGATGTTATCATGTTCGTATGTGAGAT 58.856 33.333 0.00 0.00 33.59 2.75
648 664 5.128919 ACTCATGGCTGAATCACCTAAATC 58.871 41.667 0.00 0.00 0.00 2.17
649 665 4.464008 TCATGGCTGAATCACCTAAATCC 58.536 43.478 0.00 0.00 0.00 3.01
650 666 3.297134 TGGCTGAATCACCTAAATCCC 57.703 47.619 4.12 0.00 0.00 3.85
651 667 2.852449 TGGCTGAATCACCTAAATCCCT 59.148 45.455 4.12 0.00 0.00 4.20
652 668 4.044308 TGGCTGAATCACCTAAATCCCTA 58.956 43.478 4.12 0.00 0.00 3.53
653 669 4.476846 TGGCTGAATCACCTAAATCCCTAA 59.523 41.667 4.12 0.00 0.00 2.69
654 670 5.044476 TGGCTGAATCACCTAAATCCCTAAA 60.044 40.000 4.12 0.00 0.00 1.85
655 671 6.071320 GGCTGAATCACCTAAATCCCTAAAT 58.929 40.000 0.00 0.00 0.00 1.40
661 677 5.751586 TCACCTAAATCCCTAAATCCACAC 58.248 41.667 0.00 0.00 0.00 3.82
682 698 8.181573 CCACACGCAGTAATTATTAGTCAAATT 58.818 33.333 0.00 0.00 41.61 1.82
683 699 9.554724 CACACGCAGTAATTATTAGTCAAATTT 57.445 29.630 0.00 0.00 41.61 1.82
684 700 9.554724 ACACGCAGTAATTATTAGTCAAATTTG 57.445 29.630 12.15 12.15 41.61 2.32
686 702 9.769093 ACGCAGTAATTATTAGTCAAATTTGTC 57.231 29.630 17.47 12.30 41.94 3.18
687 703 9.767684 CGCAGTAATTATTAGTCAAATTTGTCA 57.232 29.630 17.47 0.00 0.00 3.58
695 711 9.638239 TTATTAGTCAAATTTGTCAGGCATTTC 57.362 29.630 17.47 0.00 0.00 2.17
696 712 4.886579 AGTCAAATTTGTCAGGCATTTCC 58.113 39.130 17.47 0.00 0.00 3.13
697 713 4.344679 AGTCAAATTTGTCAGGCATTTCCA 59.655 37.500 17.47 0.00 37.29 3.53
699 715 5.702209 GTCAAATTTGTCAGGCATTTCCATT 59.298 36.000 17.47 0.00 37.29 3.16
700 716 5.701750 TCAAATTTGTCAGGCATTTCCATTG 59.298 36.000 17.47 0.00 37.29 2.82
715 754 7.436673 GCATTTCCATTGTTATTATAAACGGCA 59.563 33.333 0.00 0.00 31.76 5.69
872 917 2.024080 CCCCTTTCATCTCCCCATTTCA 60.024 50.000 0.00 0.00 0.00 2.69
916 961 2.200170 CTTTTCCGCTGCTTTCGGGG 62.200 60.000 10.90 3.12 46.43 5.73
942 987 2.114616 GATCTGCTCCCTCTCCAGAAA 58.885 52.381 0.00 0.00 38.89 2.52
986 1031 1.070786 ACAAGTACACCACCGCCAG 59.929 57.895 0.00 0.00 0.00 4.85
987 1032 1.070786 CAAGTACACCACCGCCAGT 59.929 57.895 0.00 0.00 0.00 4.00
1824 1895 0.806868 ATTGGCACATCTGCAACTCG 59.193 50.000 0.00 0.00 46.28 4.18
2229 2318 1.453745 GGCGATGGAGGATGGCAAA 60.454 57.895 0.00 0.00 37.52 3.68
2391 2481 0.825410 TAAAATGCCTACCCGCTCGA 59.175 50.000 0.00 0.00 0.00 4.04
2393 2483 0.035820 AAATGCCTACCCGCTCGAAA 60.036 50.000 0.00 0.00 0.00 3.46
2402 2492 1.950909 ACCCGCTCGAAAACATTTTCA 59.049 42.857 15.45 4.27 45.15 2.69
2403 2493 2.556622 ACCCGCTCGAAAACATTTTCAT 59.443 40.909 15.45 0.00 45.15 2.57
2481 2571 5.753921 CAGCTTTACTAGGCTAATAGCGTTT 59.246 40.000 12.87 3.75 43.62 3.60
2513 2603 5.619625 AGCGTATCCGTTAGTAATAGGAC 57.380 43.478 10.94 2.28 35.36 3.85
2529 2621 8.422566 AGTAATAGGACCTGTAATGTTCTAAGC 58.577 37.037 3.53 0.00 25.93 3.09
2540 2632 6.945435 TGTAATGTTCTAAGCATTTCTTCCCA 59.055 34.615 0.00 0.00 37.65 4.37
2547 2639 3.124921 ATTTCTTCCCACGCGGCG 61.125 61.111 22.36 22.36 0.00 6.46
2613 2706 8.368668 AGCAGTTCTTATATATCTTACCACACC 58.631 37.037 0.00 0.00 0.00 4.16
2615 2708 7.328737 CAGTTCTTATATATCTTACCACACCGC 59.671 40.741 0.00 0.00 0.00 5.68
2633 2726 3.325716 ACCGCCTTCCTTACTTCTTGTTA 59.674 43.478 0.00 0.00 0.00 2.41
2699 2792 6.417258 TGCTTTGATCATCCTGTTCTGATTA 58.583 36.000 0.00 0.00 32.36 1.75
2705 2798 6.385176 TGATCATCCTGTTCTGATTACTTCCT 59.615 38.462 0.00 0.00 32.36 3.36
2706 2799 5.982356 TCATCCTGTTCTGATTACTTCCTG 58.018 41.667 0.00 0.00 0.00 3.86
2723 2816 1.133025 CCTGAAGCTTGCCGGTAATTG 59.867 52.381 2.10 0.00 0.00 2.32
2897 3006 2.621526 ACCTTCGCAACTTTTACTTGGG 59.378 45.455 0.00 0.00 33.88 4.12
2951 3060 8.076178 CCTGTTCTTGTTTTAAGTTGTCATAGG 58.924 37.037 0.00 0.00 0.00 2.57
2953 3062 8.617809 TGTTCTTGTTTTAAGTTGTCATAGGTC 58.382 33.333 0.00 0.00 0.00 3.85
2998 3108 3.839490 TCCAAGGTGATTGCCAAATTGAT 59.161 39.130 0.00 0.00 37.60 2.57
3000 3110 4.393680 CCAAGGTGATTGCCAAATTGATTG 59.606 41.667 0.00 0.00 37.60 2.67
3082 3216 7.451255 ACTTGTAATTTTCATGGTGATTCCTCA 59.549 33.333 0.00 0.00 37.07 3.86
3195 3330 8.063200 AGGTTAAAATAGCTGAAAATACCCAC 57.937 34.615 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 3.205338 CATGAACCGATGAGCCAATACA 58.795 45.455 0.00 0.00 0.00 2.29
126 127 6.646653 CCCTCCTTATTTTTCAAAAAGAGTGC 59.353 38.462 1.08 0.00 0.00 4.40
127 128 7.951591 TCCCTCCTTATTTTTCAAAAAGAGTG 58.048 34.615 1.08 0.00 0.00 3.51
130 131 7.302184 TCCTCCCTCCTTATTTTTCAAAAAGA 58.698 34.615 1.08 0.00 0.00 2.52
133 134 6.016555 CCTCCTCCCTCCTTATTTTTCAAAA 58.983 40.000 0.00 0.00 0.00 2.44
148 149 5.536497 AAAAATATGTTCACCTCCTCCCT 57.464 39.130 0.00 0.00 0.00 4.20
152 153 8.957466 GCTTAAGTAAAAATATGTTCACCTCCT 58.043 33.333 4.02 0.00 0.00 3.69
172 187 8.314751 TCCTATTAGCCTTATAAGCAGCTTAAG 58.685 37.037 18.87 13.86 36.79 1.85
177 192 6.760770 CAGATCCTATTAGCCTTATAAGCAGC 59.239 42.308 6.99 6.31 0.00 5.25
206 221 3.356290 CCTCCCTTCATAAACACCCTTG 58.644 50.000 0.00 0.00 0.00 3.61
230 245 1.134848 TGTGCTTTCCCTGTTTGCAAC 60.135 47.619 0.00 0.00 35.34 4.17
238 253 4.035441 CCAATTTTGTTTGTGCTTTCCCTG 59.965 41.667 0.00 0.00 0.00 4.45
240 255 3.314913 CCCAATTTTGTTTGTGCTTTCCC 59.685 43.478 0.00 0.00 0.00 3.97
260 275 0.885879 GATTTTTCCGGTGTCACCCC 59.114 55.000 16.60 0.00 33.75 4.95
265 280 3.756434 TGGATCAAGATTTTTCCGGTGTC 59.244 43.478 0.00 0.00 0.00 3.67
273 288 5.832060 CCTAGAGGCATGGATCAAGATTTTT 59.168 40.000 0.00 0.00 0.00 1.94
274 289 5.133322 TCCTAGAGGCATGGATCAAGATTTT 59.867 40.000 0.00 0.00 34.44 1.82
277 292 3.866816 TCCTAGAGGCATGGATCAAGAT 58.133 45.455 0.00 0.00 34.44 2.40
284 299 4.477536 AGAACTATCCTAGAGGCATGGA 57.522 45.455 0.00 0.00 34.44 3.41
293 308 7.168302 CGCACTTCATTTGTAGAACTATCCTAG 59.832 40.741 0.00 0.00 0.00 3.02
349 364 3.680937 GTCGTCCCAATAAACATTGTCGA 59.319 43.478 0.00 0.00 0.00 4.20
352 367 5.975693 AATGTCGTCCCAATAAACATTGT 57.024 34.783 0.00 0.00 38.69 2.71
354 369 5.067283 GCCTAATGTCGTCCCAATAAACATT 59.933 40.000 0.00 0.00 41.83 2.71
361 376 2.806745 CGATGCCTAATGTCGTCCCAAT 60.807 50.000 0.00 0.00 0.00 3.16
363 378 0.104120 CGATGCCTAATGTCGTCCCA 59.896 55.000 0.00 0.00 0.00 4.37
368 383 1.934589 TCAACCGATGCCTAATGTCG 58.065 50.000 0.00 0.00 35.29 4.35
382 397 0.442699 GGTCTTTCGACGCATCAACC 59.557 55.000 0.00 0.00 41.16 3.77
387 402 1.359848 GTCATGGTCTTTCGACGCAT 58.640 50.000 0.00 0.00 41.16 4.73
392 407 0.669318 GTGGCGTCATGGTCTTTCGA 60.669 55.000 0.00 0.00 0.00 3.71
393 408 1.787847 GTGGCGTCATGGTCTTTCG 59.212 57.895 0.00 0.00 0.00 3.46
421 437 1.071471 CGATGCTATTCGGGGGCTT 59.929 57.895 0.00 0.00 35.50 4.35
422 438 1.821061 CTCGATGCTATTCGGGGGCT 61.821 60.000 4.83 0.00 39.56 5.19
423 439 1.374758 CTCGATGCTATTCGGGGGC 60.375 63.158 4.83 0.00 39.56 5.80
427 443 3.775202 CCCTTATCTCGATGCTATTCGG 58.225 50.000 4.83 0.00 39.56 4.30
429 445 3.182967 CGCCCTTATCTCGATGCTATTC 58.817 50.000 0.00 0.00 0.00 1.75
437 453 1.076559 TCCACCGCCCTTATCTCGA 60.077 57.895 0.00 0.00 0.00 4.04
438 454 1.107538 TCTCCACCGCCCTTATCTCG 61.108 60.000 0.00 0.00 0.00 4.04
452 468 3.385384 CTCCGTGCCTGCTCTCCA 61.385 66.667 0.00 0.00 0.00 3.86
453 469 4.154347 CCTCCGTGCCTGCTCTCC 62.154 72.222 0.00 0.00 0.00 3.71
462 478 3.607370 GAGGTTGTCCCCTCCGTGC 62.607 68.421 0.00 0.00 44.49 5.34
469 485 1.602771 GGCTACTGAGGTTGTCCCC 59.397 63.158 0.00 0.00 0.00 4.81
523 539 0.759346 GGAGTGTGGTTCTCAGTGGT 59.241 55.000 0.00 0.00 34.04 4.16
526 542 1.689273 GTCTGGAGTGTGGTTCTCAGT 59.311 52.381 0.00 0.00 34.04 3.41
528 544 1.412710 GTGTCTGGAGTGTGGTTCTCA 59.587 52.381 0.00 0.00 34.04 3.27
568 584 6.918892 TGATAACATCAATTTCCTACCACG 57.081 37.500 0.00 0.00 36.11 4.94
620 636 4.018960 AGGTGATTCAGCCATGAGTAAGTT 60.019 41.667 12.07 0.00 36.61 2.66
648 664 2.684001 TACTGCGTGTGGATTTAGGG 57.316 50.000 0.00 0.00 0.00 3.53
649 665 6.861065 ATAATTACTGCGTGTGGATTTAGG 57.139 37.500 0.00 0.00 0.00 2.69
650 666 9.042008 ACTAATAATTACTGCGTGTGGATTTAG 57.958 33.333 0.00 0.00 0.00 1.85
651 667 8.951787 ACTAATAATTACTGCGTGTGGATTTA 57.048 30.769 0.00 0.00 0.00 1.40
652 668 7.551262 TGACTAATAATTACTGCGTGTGGATTT 59.449 33.333 0.00 0.00 0.00 2.17
653 669 7.045416 TGACTAATAATTACTGCGTGTGGATT 58.955 34.615 0.00 0.00 0.00 3.01
654 670 6.578944 TGACTAATAATTACTGCGTGTGGAT 58.421 36.000 0.00 0.00 0.00 3.41
655 671 5.968254 TGACTAATAATTACTGCGTGTGGA 58.032 37.500 0.00 0.00 0.00 4.02
661 677 9.767684 TGACAAATTTGACTAATAATTACTGCG 57.232 29.630 24.64 0.00 0.00 5.18
682 698 5.999205 ATAACAATGGAAATGCCTGACAA 57.001 34.783 0.00 0.00 37.63 3.18
683 699 5.999205 AATAACAATGGAAATGCCTGACA 57.001 34.783 0.00 0.00 37.63 3.58
686 702 8.967218 CGTTTATAATAACAATGGAAATGCCTG 58.033 33.333 0.00 0.00 37.63 4.85
687 703 8.141268 CCGTTTATAATAACAATGGAAATGCCT 58.859 33.333 0.00 0.00 37.63 4.75
688 704 7.095816 GCCGTTTATAATAACAATGGAAATGCC 60.096 37.037 0.00 0.00 37.10 4.40
689 705 7.436673 TGCCGTTTATAATAACAATGGAAATGC 59.563 33.333 0.00 0.00 0.00 3.56
690 706 8.864069 TGCCGTTTATAATAACAATGGAAATG 57.136 30.769 0.00 0.00 0.00 2.32
691 707 9.528018 CTTGCCGTTTATAATAACAATGGAAAT 57.472 29.630 0.00 0.00 0.00 2.17
692 708 8.740906 TCTTGCCGTTTATAATAACAATGGAAA 58.259 29.630 0.00 0.00 0.00 3.13
693 709 8.282455 TCTTGCCGTTTATAATAACAATGGAA 57.718 30.769 0.00 0.00 0.00 3.53
694 710 7.771361 TCTCTTGCCGTTTATAATAACAATGGA 59.229 33.333 0.00 0.00 0.00 3.41
695 711 7.925993 TCTCTTGCCGTTTATAATAACAATGG 58.074 34.615 0.00 0.00 0.00 3.16
696 712 8.612619 ACTCTCTTGCCGTTTATAATAACAATG 58.387 33.333 0.00 0.00 0.00 2.82
697 713 8.732746 ACTCTCTTGCCGTTTATAATAACAAT 57.267 30.769 0.00 0.00 0.00 2.71
699 715 9.472361 GATACTCTCTTGCCGTTTATAATAACA 57.528 33.333 0.00 0.00 0.00 2.41
700 716 9.694137 AGATACTCTCTTGCCGTTTATAATAAC 57.306 33.333 0.00 0.00 0.00 1.89
715 754 5.690464 AGAATGCAACCAGATACTCTCTT 57.310 39.130 0.00 0.00 29.16 2.85
872 917 2.770048 CTGCTCCGGGGGAAGGAT 60.770 66.667 1.90 0.00 37.13 3.24
916 961 0.467290 AGAGGGAGCAGATCGGAGTC 60.467 60.000 0.00 0.00 0.00 3.36
942 987 2.284995 GGTCTGGCAGAGGAGGGT 60.285 66.667 19.38 0.00 0.00 4.34
2220 2309 0.463833 CCCCGTACTCTTTGCCATCC 60.464 60.000 0.00 0.00 0.00 3.51
2391 2481 9.202273 ACGCAAACACATATATGAAAATGTTTT 57.798 25.926 20.91 10.64 37.99 2.43
2393 2483 8.755696 AACGCAAACACATATATGAAAATGTT 57.244 26.923 19.63 14.99 34.12 2.71
2403 2493 9.609950 GTTAAACCTTAAACGCAAACACATATA 57.390 29.630 0.00 0.00 0.00 0.86
2481 2571 3.153024 GGATACGCTTGTGCTTCCA 57.847 52.632 0.00 0.00 36.97 3.53
2513 2603 7.415653 GGGAAGAAATGCTTAGAACATTACAGG 60.416 40.741 0.00 0.00 36.74 4.00
2529 2621 2.485122 GCCGCGTGGGAAGAAATG 59.515 61.111 18.41 0.00 38.47 2.32
2540 2632 2.890847 CTTCTCATTCCTCGCCGCGT 62.891 60.000 13.39 0.00 0.00 6.01
2547 2639 6.227298 TGGAATAGTGACTTCTCATTCCTC 57.773 41.667 19.91 2.38 35.40 3.71
2612 2705 2.474410 ACAAGAAGTAAGGAAGGCGG 57.526 50.000 0.00 0.00 0.00 6.13
2613 2706 4.566987 ACTAACAAGAAGTAAGGAAGGCG 58.433 43.478 0.00 0.00 0.00 5.52
2615 2708 8.804204 TCTCTAACTAACAAGAAGTAAGGAAGG 58.196 37.037 0.00 0.00 0.00 3.46
2699 2792 1.302832 CCGGCAAGCTTCAGGAAGT 60.303 57.895 10.47 0.00 40.45 3.01
2705 2798 1.173043 CCAATTACCGGCAAGCTTCA 58.827 50.000 0.00 0.00 0.00 3.02
2723 2816 7.693952 TCAAGTTAATGTAAAGATGAATCGCC 58.306 34.615 0.00 0.00 0.00 5.54
2760 2853 4.098807 CCATGATGCCATCAAACTTCATCA 59.901 41.667 12.08 5.80 44.88 3.07
2897 3006 2.791004 GTGTGCTGAAACTCAATGCAAC 59.209 45.455 0.00 0.00 30.89 4.17
2951 3060 9.880064 GAATTCTGAAGGTAAGTTAAAAGTGAC 57.120 33.333 0.00 0.00 0.00 3.67
2953 3062 8.846211 TGGAATTCTGAAGGTAAGTTAAAAGTG 58.154 33.333 5.23 0.00 0.00 3.16
2961 3070 5.073144 TCACCTTGGAATTCTGAAGGTAAGT 59.927 40.000 27.81 13.21 46.30 2.24
3043 3155 9.376075 TGAAAATTACAAGTGAAAAGATTTGCA 57.624 25.926 0.00 0.00 0.00 4.08
3195 3330 3.824414 AGTTTAAAATGAGGCGGTTCG 57.176 42.857 0.00 0.00 0.00 3.95


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.